Blog Archive

Monday, 16 June 2008

Weekly BioNews 9 - 16 June 2008

Salmonella is serving up a surprise not only for tomato lovers around the country but also for scientists who study the rod-shaped bacterium that causes misery for millions of people.

In research published June 4 in the online journal PloS One, researchers say they've identified a molecular trick that may explain part of the bacteria's fierceness. A team from the University of Rochester Medical Center has identified a protein that allows the bacteria to maintain a low profile in the body, giving the bacteria crucial time to quietly gain a foothold in an organism before the immune system is roused to fight the invader.

"Inflammation immediately after a bacterial infection occurs helps the body fight off bugs like Salmonella quickly," said Jun Sun, Ph.D., the leader of the team and assistant professor of Gastroenterology and Hepatology. "But it may be that Salmonella is especially equipped with tools to allow it to evade the immune system early on, growing quietly and then really making the host quite ill. Salmonella is trickier than we imagined."

Sun's team found that a virulence protein known as AvrA dampens the inflammatory response. That helps the bacteria avoid the wrath of the immune system and gives the infection crucial time to grow and develop before it needs to expend energy to fight off immune cells like neutrophils, which would attack the intruder more quickly if the bacteria attacked the body in a more clear-cut fashion.

"AvrA allows Salmonella to make peace with you, buying the bacteria a little time to survive in the body," said Sun. "That's bad news for the body, because then the bacteria spreads. AvrA allows the bacteria to do harm in the body without the body realizing it. Bacteria have been evolving for millions of years. That gives them some tricks that perhaps we don't understand yet."

AvrA is one of several proteins in Salmonella that affect cells in the wall of the intestines and stomach known as epithelial cells. These cells link up tightly together thanks to molecules known as tight junction proteins, which form an elaborate barrier to keep molecules and substances in or out of the colon. The bacterium employs several proteins enabling it to loosen these junctions, effectively breaking up the barrier and making the body vulnerable to the infection.

While several of Salmonella's proteins allow it to loosen up and punch through this latticework, Sun's team unexpectedly found that AvrA allows the bacteria to maintain these tight junctions. This ability reduces the body's inflammatory response and allows the bacteria to avoid detection by the immune system for some time, enabling the bacteria to survive in the host. The severe symptoms of infection, including nausea, vomiting, diarrhea, and abdominal cramps, typically hit anywhere from 8 to 72 hours after initial exposure to the bug.....

A large genetic study of the extinct woolly mammoth has revealed that the species was not one large homogenous group, as scientists previously had assumed, and that it did not have much genetic diversity.

"The population was split into two groups, then one of the groups died out 45,000 years ago, long before the first humans began to appear in the region," said Stephan C. Schuster, associate professor of biochemistry and molecular biology at Penn State University and a leader of the research team. "This discovery is particularly interesting because it rules out human hunting as a contributing factor, leaving climate change and disease as the most probable causes of extinction."

The discovery will be published later this week in the early online edition of the Proceedings of the National Academy of Sciences (PNAS).

The research marks the first time scientists have dissected the structure of an entire population of extinct mammal by using the complete mitochondrial genome -- all the DNA that makes up all the genes found in the mitochondria structures within cells. Data from this study will enable testing of the new hypothesis presented by the team, that there were two groups of woolly mammoth -- a concept that previously had not been recognized from studies of the fossil record.The scientists analyzed the genes in hair obtained from individual woolly mammoths -- an extinct species of elephant adapted to living in the cold environment of the northern hemisphere. The bodies of these mammoths were found throughout a wide swathe of northern Siberia. Their dates of death span roughly 47,000 years, ranging from about 13,000 years ago to about 60,000 years ago.

Schuster and Webb Miller, professor of biology and computer science and engineering at Penn State, led the international research team, which includes Thomas Gilbert at the University of Copenhagen in Denmark and other scientists in Australia, Belgium, France, Italy, Russia, Spain, Sweden, the United Kingdom, and the United States. The team includes experts in the fields of genome evolution, ancient DNA, and mammoth paleontology, as well as curators from various natural-history museums....

MIT researchers have figured out how bacteria ensure that they respond correctly to hundreds of incoming signals from their environment.

The researchers also successfully rewired the cellular communications pathways that control those responses, raising the possibility of engineering bacteria that can serve as biosensors to detect chemical pollutants. The work is reported in the June 13 issue of Cell.

Led by MIT biology professor Michael Laub, the team studied genomes of nearly 200 bacteria, which can have hundreds of different pathways that respond to different types of external stimuli. Nutrients, antibiotics, temperature or light can evoke a variety of responses, including transcription of particular genes.

In most cases, the pathways involve two proteins. The first protein, an enzyme known as a histidine kinase, receives the external signal and then activates the second protein, known as a response regulator.

It's critical that each histidine kinase activate only the appropriate response regulator. Different histidine kinases are often very structurally similar, as are the response regulator proteins, so scientists have wondered how cells prevent signals from getting crossed.

"If an organism has tons of this class of signaling pathway, why do we not get a lot of crosstalk?" said Laub. "How does the kinase pick out the right target?"

Based on earlier studies, the MIT researchers theorized that the specificity of the interaction is determined by a subset of amino acids on the histidine kinase and a corresponding subset of amino acids on the response regulator.

To confirm their theory, they looked for patterns of amino acid co-evolution in pairs of histidine kinases and their target response regulators.

Co-evolution occurs when a mutation in one of the two proteins is followed by a secondary mutation in the corresponding amino acid on the other protein, allowing the protein pair to maintain their interaction.

After searching a vast database of nearly 1,300 protein pairs, they identified a small set of co-evolved amino acids. They then confirmed that these amino acids govern signaling specificity by successfully rewiring five of the pathways by mutating the target amino acids....

Diagram shows the structure of a histidine kinase (blue ribbons) and its target response regulator (green ribbons). The specificity of the interaction between the two proteins is primarily determined by the orange and red amino acid residues. (Credit: Image / Protein Data Bank, Michael Laub and Jeffrey Skerker)

The proteins upon which life depends share an attribute with paper airplanes: Unless folded properly, they just won't fly.But researchers have been puzzled by how the long, linear proteins cranked out by the ribosome factories in a cell are folded into the shapes they must assume to perform their function. They only have known that for many of the most complex and essential proteins, the folding takes place out of sight, hidden in the inner cavity of a type of molecule called a chaperonin.

Now Stanford researchers have begun prying open the lid, literally, on the inner workings of chaperonin molecules by deducing the mechanism by which the lid operates on a barrel-shaped chaperonin called TRiC.

"Understanding how the lid opens and closes really helps us understand how everything moves inside the chaperonin," said Judith Frydman, associate professor of biology and one of two senior authors of a paper published online this week in Nature Structural & Molecular Biology.

"This is just the beginning, but now we can start to understand how the protein is pushed inside the cavity of the chaperonin and what this folding chamber looks like," Frydman said. Learning how a protein is manipulated inside TRiC while it is being folded is a crucial step in Frydman's larger plan.

"Our goal is to eventually exert control," she said. "If we could re-engineer the chaperonin to either fold better misfolded proteins or alternatively to remove them from circulation, then we could prevent those proteins from being harmful to cells."

Misfolded proteins have been implicated in a number of diseases, including some cancers, as well as ailments related to aging, such as Alzheimer's and Parkinson's diseases.

"Folding is one of the key steps for the health of the cell," Frydman said.

Virtually all proteins have to be folded-some in complex configurations-in order to function properly, and many are known to require a molecule called a chaperone to fold them. Frydman estimates that perhaps 10 percent of the proteins needing chaperones must have one that, like TRiC, is part of the subset called chaperonins. Other work done in Frydman's lab has shown that proteins that have very complex folds seem to require chaperonins.

"Many of the proteins that have these complex folds are the most important ones for life," Frydman said. "The proteins that control the cell cycle, tumor suppressers and the proteins that control the shape of the cell are dependent on chaperonins to get to the folded state.

"If the chaperones don't work well, then all these proteins that have been made become toxic," she said.

TRiC, like all chaperonins, consists of a double-ringed structure that gives it a barrel shape. One ring opens to admit the raw protein into the inner recesses of the folding machine, then closes tightly while, inside the chaperonin "black box," the mysteries of molecular origami unfold-or, more correctly, fold. Upon completion of the folding, the ring at the other end opens up to push out the finished product.

"It is really like a nanomachine. It closes off, the protein is trapped inside and something-we don't understand what-happens inside this chamber, and the protein comes out folded," Frydman said. "It is a very complex mechanism."

The rings at each end of the barrel have to synchronize their actions for the sequence of events to happen correctly.

"We don't know how the rings coordinate," Frydman said. "What we have is evidence that this machine works like a two-stroke motor, so that opening one ring closes the other, and when that other ring opens, the first one is closed."

Timing is critical because if a protein does not stay in the chaperonin long enough, it may not have time to fold properly. Conversely, if it lingers too long, it may also fold incorrectly. And sometimes proteins are not made correctly by the ribosome, so they simply do not bind well to their chaperone, making proper folding impossible....

By disrupting the potassium channel of the malaria parasite, a team of researchers has been able to prevent the malaria parasites from forming in mosquitoes and has thereby broken the cycle of infection during recent animal tests.By genetically altering the malaria parasite through gene knock-out technology, a research team consisting of scientists at the University of Copenhagen and John Hopkins University, Baltimore, has prevented the parasite from going through the normal stages of its life cycle and developing a cyst (egg-like structure or occyst), which spawns new infectious parasites." As it is exclusively the parasites from these oocysts that can infect new individuals, we were able to prevent the disease from being transmitted to theanimals in our tests", explains Assistant Professor, Peter Ellekvist from the University of Copenhagen.

The findings have been published in the scientific journal Proceedings of the National Academy of Sciences, USA, (2008 105: 6398-6402).The intervention "disrupts" the parasites complex life cycle

The malaria parasite has an extremely complicated lifecycle, which starts with the fertilisation of the parasites male and female gametes and the formation of an oocyst, in the mosquito's stomach wall. The oocyst further develops into sporozoittes, which travel up the mosquito's salivary gland and from there are transmitted to people, when the mosquito secures its next blood meal. After residing for a short period in the liver cells, the parasites then infect the red blood cells, thereby wreaking havoc in the human body. The malaria parasites are able to reproduce both through sexual reproduction when they inhabit a mosquito (and are transmitted to the host) and via asexual reproduction when they reside in the human body (replication in the host). For scientists to successfully counteract malaria, they must tackle both the transmission from person to person by the mosquitoes and the spread of the malaria parasites in the infected individual.The potassium channels are important for all cells

All animal and plant cells contain so-called ion channels. These are small pores which allow ions to move in and out through an otherwiseimpermeable cell membrane. The potassium channels are a sub-type of ion channel, found in all cells. Though the function of the potassium channels vary, they play a crucial role in a variety of biological processes, e.g. influencing the ability of the nerves to send electrical signals and the heart muscle to contract rhythmically.

Assistant Professor Peter Ellekvist explains that his interest in malaria led to a research collaboration with Professor Dan Klærke, who studies potassium channels at the University of Copenhagen. In collaboration with Professor Nirbhay Kumar and other colleagues from the Malaria Research Institute at John Hopkins University in Baltimore, the two researchers were able to manipulate the parasite's genes so as to ensure that the potassium channel no longer functioned. To their surprise, however, this intervention did not, in the first instance, appear to have any effect on the parasites....

A single organ may contain more than one type of adult stem cell - a discovery that complicates prospects for using the versatile cells to replace damaged tissue as a treatment for disease, according to a new study from the laboratory of geneticist Mario Capecchi, the University of Utah's Nobel Laureate.In the June 8 online issue of the journal Nature Genetics, Capecchi and geneticist Eugenio Sangiorgi report that when they used a gene named Bmi1 to mark the presence of adult stem cells in the intestines of mice, they were surprised to find the specific cells mostly in the upper third of the mouse intestine.

That indicates at least one or two other types of adult stem cells must exist to maintain and repair the middle and lower thirds of the mouse's guts. The small intestine in a mouse is almost 12 inches long if stretched from end to end.

Adult stem cells are "undifferentiated" cells that can become any type of cell in the organ in which they are found. Medical researchers hope to transplant adult stem cells to treat various diseases. Examples include placing adult stem cells in the pancreas to replace damaged insulin-producing cells, in the heart to replace cardiac muscle cells killed by heart attack, and in the brain to replace dopamine-producing cells damaged in Parkinson's disease patients.

The new discovery "is important because people are talking about stem cell therapy; they want to stick in stem cells to treat disease," says Capecchi, a winner of the 2007 Nobel Prize in Physiology or Medicine.

"People always thought about a uniform stem cell population in each organ, but now we are saying there are multiple stem cell populations in a given organ, so if you're going to do therapy, you have to recognise this complexity," adds Capecchi, co-chair and distinguished professor of human genetics at the University of Utah and an investigator with the Howard Hughes Medical Institute.Sangiorgi, a postdoctoral fellow in human genetics, adds: "There are probably different stem cells in the small intestine doing different things."

If more than one kind of adult stem cell is required to generate the intestinal lining, "it wouldn't be surprising to see it is true for other organs as well," Capecchi says.

Adult stem cells have been seen as an alternative to embryonic stem cells, which are able to become any kind of cell in the body - not just in a given organ - and are obtained from test-tube fertilisation of eggs left over by couples attempting to have babies. Embryonic stem cells have been controversial because abortion foes consider them to be human beings rather than a small batch of cells.

Capecchi won the Nobel - with Sir Martin Evans and Oliver Smithies - for developing gene targeting, a method of using embryonic stem cells to "knock out" genes in mice, then observing what goes wrong to determine any gene's normal function.

Getting to the Guts of Adult Stem Cells

Stem cells in the intestine are among the best studied. They are required to produce new cells for the intestinal lining as older ones wear out every two to five days.

"It's a hell of an environment," Capecchi says. "Food is being thrown in there, and enzymes to break down that food. This is a way of maintaining the intestine intact."

The intestinal adult stem cells give rise to various cells in the small intestine: cells to absorb foods; cells to secrete mucus that make the lining smooth and protect it; cells involved in protecting the organism against bacteria and other disease organisms; and cells that produce substances involved in communication among cells.

But researchers have had trouble identifying the stem cells so they can be studied.

"Adult stem cells are a giant black box," Sangiorgi says.

Hijacking a Gene to Unveil Stem Cells

Dutch researchers recently found a "marker" named Lgr5 to label intestinal stem cells. Sangiorgi and Capecchi used a similar method but a different "marker" - a gene name Bmi1 - which is "expressed" or activated in adult stem cells in the intestinal lining.

Labelling stem cells containing the Bmi1 gene involved tamoxifen, a drug used to treat and prevent breast cancer. Tamoxifen was used to activate an enzyme in cells that contain the Bmi1 gene so that the cells appeared blue when viewed under a microscope...